Before a probe can be used to scan a sample, its position relative to the x-y stage on which the sample is mounted must be known. The microscope generally knows the location of the probe tip within an initial level of uncertainty (a). In prior art microscopes, the initial level of uncertainty (a) can be large. The level of uncertainty (a) should, however, correspond to the precision of the stage, which is generally a few microns. A probe tip locator is used to more precisely determine the location of the probe tip, i.e., reduce the level of uncertainty (a) to an acceptable target value. The probe tip locator is placed at a predetermined location on the stage. The locator is designed so that a scan of the locator will provide information about the position of the probe over the locator. Using this information, the position of the probe tip relative to the microscope stage and scan actuator can be determined.